From 3987611b67974ef0f32ff5521295ff77eb7d0f0b Mon Sep 17 00:00:00 2001
From: Lavinia Baumstark <baumstark@pik-potsdam.de>
Date: Tue, 14 Jan 2020 11:44:54 +0100
Subject: [PATCH] remove start_functions.R, adapt start_bundle_climate.R
---
scripts/start_functions.R | 489 --------------------------------------
start_bundle_climate.R | 10 +-
2 files changed, 8 insertions(+), 491 deletions(-)
delete mode 100644 scripts/start_functions.R
diff --git a/scripts/start_functions.R b/scripts/start_functions.R
deleted file mode 100644
index c7bbb7e..0000000
--- a/scripts/start_functions.R
+++ /dev/null
@@ -1,489 +0,0 @@
-# | (C) 2006-2019 Potsdam Institute for Climate Impact Research (PIK)
-# | authors, and contributors see CITATION.cff file. This file is part
-# | of REMIND and licensed under AGPL-3.0-or-later. Under Section 7 of
-# | AGPL-3.0, you are granted additional permissions described in the
-# | REMIND License Exception, version 1.0 (see LICENSE file).
-# | Contact: remind@pik-potsdam.de
-start_run <- function(cfg, scenario = NULL, report = NULL, sceninreport = NULL, coupled = F, force = FALSE) {
-
- # Load libraries
- require(lucode, quietly = TRUE,warn.conflicts =FALSE)
- require(magclass, quietly = TRUE,warn.conflicts =FALSE)
- require(tools, quietly = TRUE,warn.conflicts =FALSE)
- require(remind, quietly = TRUE,warn.conflicts =FALSE)
- require(moinput)
- require(mrvalidation)
-
- .copy.fromlist <- function(filelist,destfolder) {
- if(is.null(names(filelist))) names(filelist) <- rep("",length(filelist))
- for(i in 1:length(filelist)) {
- if(!is.na(filelist[i])) {
- to <- paste0(destfolder,"/",names(filelist)[i])
- if(!file.copy(filelist[i],to=to,recursive=dir.exists(to),overwrite=T))
- cat(paste0("Could not copy ",filelist[i]," to ",to,"\n"))
- }
- }
- }
-
- # Store REMIND-root directory
- maindir <- getwd()
- on.exit(setwd(maindir))
-
- # Is the run performed on the cluster?
- on_cluster <- file.exists('/p')
-
- # Adapt configuration to predifined scenario, if given
- if(!is.null(scenario))
- cfg <- setScenario(cfg, scenario)
-
- # Check configuration for consistency
- cfg <- check_config(cfg, settings_config = "config/settings_config.csv")
-
-
-###-------- do update of input files based on previous runs if applicable ------###
- if(!is.null(cfg$gms$carbonprice) && (cfg$gms$carbonprice == "NDC2018")){
- source("scripts/input/prepare_NDC2018.R")
- prepare_NDC2018(as.character(cfg$files2export$start["input_ref.gdx"]))
- }
- ## the following is outcommented because by now it has to be done by hand ( currently only one gdx is handed to the next run, so it is impossible to fix to one run and use the tax from another run)
- ## Update CO2 tax information for exogenous carbon price runs with the same CO2 price as a previous run
- #if(!is.null(cfg$gms$carbonprice) && (cfg$gms$carbonprice == "ExogSameAsPrevious")){
- # source("scripts/input/create_ExogSameAsPrevious_CO2price_file.R")
- # create_ExogSameAsPrevious_CO2price_file(as.character(cfg$files2export$start["input_ref.gdx"]))
- #}
-
- #AJS
- if ( (cfg$gms$optimization != 'nash') & (cfg$gms$subsidizeLearning == 'globallyOptimal') ) {
- cat("Only optimization='nash' is compatible with subsudizeLearning='globallyOptimal'. Switching subsidizeLearning to 'off' now. \n")
- cfg$gms$subsidizeLearning = 'off'
- }
- # reportCEScalib only works with the calibrate module
- if ( cfg$gms$CES_parameters != "calibrate" ) cfg$output <- setdiff(cfg$output,"reportCEScalib")
-
- #AJS quit if title is too long - GAMS can't handle that
- if( nchar(cfg$title) > 75 | grepl("\\.",cfg$title) ) {
- stop("This title is too long or the name contains dots - GAMS would not tolerate this, and quit working at a point where you least expect it. Stopping now. ")
- }
-
- # Calculate CES configuration string
- cfg$gms$cm_CES_configuration <- paste0("stat_",cfg$gms$stationary,"-",
- "indu_",cfg$gms$industry,"-",
- "buil_",cfg$gms$buildings,"-",
- "tran_",cfg$gms$transport,"-",
- "POP_", cfg$gms$cm_POPscen, "-",
- "GDP_", cfg$gms$cm_GDPscen, "-",
- "Kap_", cfg$gms$capitalMarket, "-",
- "Reg_", substr(regionscode(cfg$regionmapping),1,10))
-
- # write name of corresponding CES file to datainput.gms
- replace_in_file(file = "./modules/29_CES_parameters/load/datainput.gms",
- content = paste0('$include "./modules/29_CES_parameters/load/input/',cfg$gms$cm_CES_configuration,'.inc"'),
- subject = "CES INPUT")
-
- # adjust GDPpcScen based on GDPscen
- cfg$gms$c_GDPpcScen <- gsub("gdp_","",cfg$gms$cm_GDPscen)
-
- # Make sure all MAGICC files have LF line endings, so Fortran won't crash
- if (on_cluster)
- system("find ./core/magicc/ -type f | xargs dos2unix -q")
-
- # Set source_include so that loaded scripts know they are included as
- # source (instead a load from command line)
- source_include <- TRUE
-
- ################## M O D E L L O C K ###################################
- # Lock the directory for other instances of the start scritps
- lock_id <- model_lock(timeout1 = 1, oncluster=on_cluster)
- on.exit(model_unlock(lock_id, oncluster=on_cluster))
- ################## M O D E L L O C K ###################################
-
- # If report and scenname are supplied the data of this scenario in the report will be converted to REMIND input
- # Used for REMIND-MAgPIE coupling
- if (!is.null(report) && !is.null(sceninreport)) {
- getReportData(report,sceninreport,inputpath_mag=cfg$gms$biomass,inputpath_acc=cfg$gms$agCosts)
- }
-
- # Update module paths in GAMS code
- update_modules_embedding()
-
- # configure main model gms file (cfg$model) based on settings of cfg file
- cfg$gms$c_expname <- cfg$title
- # run main.gms if not further specified
- if(is.null(cfg$model)) cfg$model <- "main.gms"
- manipulateConfig(cfg$model, cfg$gms)
-
- # Check all setglobal settings for consistency
- settingsCheck()
-
- ###########################################################################################################
- ############# PROCESSING INPUT DATA ###################### START ##########################################
- ###########################################################################################################
-
-
- ########## declare functions for updating information ################
- update_info <- function(regionscode,revision) {
-
- subject <- 'VERSION INFO'
- content <- c('',
- paste('Regionscode:',regionscode),
- '',
- paste('Input data revision:',revision),
- '',
- paste('Last modification (input data):',date()),
- '')
- replace_in_file(cfg$model,paste('*',content),subject)
- }
-
- update_sets <- function(map) {
- .tmp <- function(x,prefix="", suffix1="", suffix2=" /", collapse=",", n=10) {
- content <- NULL
- tmp <- lapply(split(x, ceiling(seq_along(x)/n)),paste,collapse=collapse)
- end <- suffix1
- for(i in 1:length(tmp)) {
- if(i==length(tmp)) end <- suffix2
- content <- c(content,paste0(' ',prefix,tmp[[i]],end))
- }
- return(content)
- }
- modification_warning <- c(
- '*** THIS CODE IS CREATED AUTOMATICALLY, DO NOT MODIFY THESE LINES DIRECTLY',
- '*** ANY DIRECT MODIFICATION WILL BE LOST AFTER NEXT INPUT DOWNLOAD',
- '*** CHANGES CAN BE DONE USING THE RESPECTIVE LINES IN scripts/start_functions.R')
- content <- c(modification_warning,'','sets')
- # write iso set with nice formatting (10 countries per line)
- tmp <- lapply(split(map$CountryCode, ceiling(seq_along(map$CountryCode)/10)),paste,collapse=",")
- regions <- levels(map$RegionCode)
- content <- c(content, '',paste(' all_regi "all regions" /',paste(regions,collapse=','),'/',sep=''),'')
- # Creating sets for H12 subregions
- subsets <- toolRegionSubsets(map=cfg$regionmapping)
- if(is.null(subsets[["EUR"]]))
- subsets[["EUR"]] <- c("EUR")
- content <- c(content, paste(' ext_regi "extended regions list (includes subsets of H12 regions)" / ', paste(c(paste0(names(subsets),"_regi"),regions),collapse=','),' /',sep=''),'')
- content <- c(content, ' regi_group(ext_regi,all_regi) "region groups (regions that together corresponds to a H12 region)"')
- content <- c(content, ' /')
- for (i in 1:length(subsets)){
- content <- c(content, paste0(' ', paste(c(paste0(names(subsets)[i],"_regi"))), ' .(',paste(subsets[[i]],collapse=','), ')'))
- }
- content <- c(content, ' /')
- content <- c(content, ' ')
- # iso countries set
- content <- c(content,' iso "list of iso countries" /')
- content <- c(content, .tmp(map$CountryCode, suffix1=",", suffix2=" /"),'')
- content <- c(content,' regi2iso(all_regi,iso) "mapping regions to iso countries"',' /')
- for(i in levels(map$RegionCode)) {
- content <- c(content, .tmp(map$CountryCode[map$RegionCode==i], prefix=paste0(i," . ("), suffix1=")", suffix2=")"))
- }
- content <- c(content,' /')
- content <- c(content, 'iso_regi "all iso countries and EU and greater China region" / EUR,CHA,')
- content <- c(content, .tmp(map$CountryCode, suffix1=",", suffix2=" /"),'')
- content <- c(content,' map_iso_regi(iso_regi,all_regi) "mapping from iso countries to regions that represent country" ',' /')
- for(i in regions[regions %in% c("EUR","CHA",levels(map$CountryCode))]) {
- content <- c(content, .tmp(i, prefix=paste0(i," . "), suffix1="", suffix2=""))
- }
- content <- c(content,' /',';')
- replace_in_file('core/sets.gms',content,"SETS",comment="***")
- }
-
- ############### download and distribute input data ###################
- # check wheather the regional resolution and input data revision are outdated and update data if needed
- if(file.exists("input/source_files.log")) {
- input_old <- readLines("input/source_files.log")[1]
- } else {
- input_old <- "no_data"
- }
- input_new <- paste0("rev",cfg$revision,"_", regionscode(cfg$regionmapping),"_", tolower(cfg$model_name),".tgz")
-
- if(!setequal(input_new, input_old) | cfg$force_download) {
- cat("Your input data are outdated or in a different regional resolution. New data are downloaded and distributed. \n")
- download_distribute(files = input_new,
- repositories = cfg$repositories, # defined in your local .Rprofile or on the cluster /p/projects/rd3mod/R/.Rprofile
- modelfolder = ".",
- debug = FALSE)
- }
-
- ##################### update information #############################
- # update_info, which regional resolution and input data revision in cfg$model
- update_info(regionscode(cfg$regionmapping),cfg$revision)
- # update_sets, which is updating the region-depending sets in core/sets.gms
- #-- load new mapping information
- map <- read.csv(cfg$regionmapping,sep=";")
- update_sets(map)
-
- ###########################################################################################################
- ############# PROCESSING INPUT DATA ###################### END ############################################
- ###########################################################################################################
-
-
- ############# ADD MODULE INFO IN SETS ###################### START ##########################################
- content <- NULL
- modification_warning <- c(
- '*** THIS CODE IS CREATED AUTOMATICALLY, DO NOT MODIFY THESE LINES DIRECTLY',
- '*** ANY DIRECT MODIFICATION WILL BE LOST AFTER NEXT MODEL START',
- '*** CHANGES CAN BE DONE USING THE RESPECTIVE LINES IN scripts/start_functions.R')
- content <- c(modification_warning,'','sets')
- content <- c(content,'',' modules "all the available modules"')
- content <- c(content,' /',paste0(" ",getModules("modules/")[,"name"]),' /')
- content <- c(content,'','module2realisation(modules,*) "mapping of modules and active realisations" /')
- content <- c(content,paste0(" ",getModules("modules/")[,"name"]," . %",getModules("modules/")[,"name"],"%"))
- content <- c(content,' /',';')
- replace_in_file('core/sets.gms',content,"MODULES",comment="***")
- ############# ADD MODULE INFO IN SETS ###################### END ############################################
-
- # Replace load leveler-script with appropriate version
- if (cfg$gms$optimization == "nash" && cfg$gms$cm_nash_mode == "parallel") {
- if(length(unique(map$RegionCode)) <= 12) {
- cfg$files2export$start[cfg$files2export$start == "scripts/run_submit/submit.cmd"] <-
- "scripts/run_submit/submit_par.cmd"
- } else { # use max amount of cores if regions number is greater than 12
- cfg$files2export$start[cfg$files2export$start == "scripts/run_submit/submit.cmd"] <-
- "scripts/run_submit/submit_par16.cmd"
- }
- } else if (cfg$gms$optimization == "testOneRegi") {
- cfg$files2export$start[cfg$files2export$start == "scripts/run_submit/submit.cmd"] <-
- "scripts/run_submit/submit_short.cmd"
- }
-
- # choose which conopt files to copy
- cfg$files2export$start <- sub("conopt3",cfg$gms$cm_conoptv,cfg$files2export$start)
-
- # Create name of output folder and output folder itself
- date <- format(Sys.time(), "_%Y-%m-%d_%H.%M.%S")
- cfg$results_folder <- gsub(":date:", date, cfg$results_folder, fixed = TRUE)
- cfg$results_folder <- gsub(":title:", cfg$title, cfg$results_folder, fixed = TRUE)
- # Create output folder
- if (!file.exists(cfg$results_folder)) {
- dir.create(cfg$results_folder, recursive = TRUE, showWarnings = FALSE)
- } else if (!force) {
- stop(paste0("Results folder ",cfg$results_folder," could not be created because it already exists."))
- } else {
- cat("Deleting results folder because it alreay exists:",cfg$results_folder,"\n")
- unlink(cfg$results_folder, recursive = TRUE)
- dir.create(cfg$results_folder, recursive = TRUE, showWarnings = FALSE)
- }
-
- # Copy important files into output_folder (before REMIND execution)
- .copy.fromlist(cfg$files2export$start,cfg$results_folder)
-
- # Store main folder to make it accessible in submit.R
- cfg$remind_folder <- getwd()
-
- # Save configuration
- save(cfg, file = path(cfg$results_folder, "config.Rdata"))
-
- # Merge GAMS files
- singleGAMSfile(mainfile=cfg$model,output = path(cfg$results_folder, "full.gms"))
-
- # Collect run statistics (will be saved to central database in submit.R)
- lucode::runstatistics(file = paste0(cfg$results_folder,"/runstatistics.rda"),
- user = Sys.info()[["user"]],
- date = Sys.time(),
- version_management = "git",
- revision = try(system("git rev-parse --short HEAD", intern=TRUE), silent=TRUE),
- #revision_date = try(as.POSIXct(system("git show -s --format=%ci", intern=TRUE), silent=TRUE)),
- status = try(system("git status", intern=TRUE), silent=TRUE))
-
- ################## M O D E L U N L O C K ###################################
- # After full.gms was produced remind folders have to be unlocked to allow setting up the next run
- model_unlock(lock_id, oncluster=on_cluster)
- # Prevent model_unlock from being executed again at the end
- on.exit()
- # Repeat command since on.exit was cleared
- on.exit(setwd(maindir))
- ################## M O D E L U N L O C K ###################################
-
- setwd(cfg$results_folder)
-
- # Decide whether the runs should be send to slurm (TRUE) or executed directly (FALSE)
- if (is.na(cfg$sendToSlurm)) {
- if (on_cluster) {
- cfg$sendToSlurm <- TRUE
- } else {
- cfg$sendToSlurm <- FALSE
- }
- }
-
- # "Compilation only" is always executed directly
- if (cfg$action == "c") cfg$sendToSlurm <- FALSE
-
- # Call appropriate submit script
- if (cfg$sendToSlurm) {
- # send to slurm
- if(cfg$gms$optimization == "nash" && cfg$gms$cm_nash_mode == "parallel") {
- if(length(unique(map$RegionCode)) <= 12) {
- system(paste0("sed -i 's/__JOB_NAME__/pREMIND_", cfg$title,"/g' submit_par.cmd"))
- system("sbatch submit_par.cmd")
- } else { # use max amount of cores if regions number is greater than 12
- system(paste0("sed -i 's/__JOB_NAME__/pREMIND_", cfg$title,"/g' submit_par16.cmd"))
- system("sbatch submit_par16.cmd")
- }
- } else if (cfg$gms$optimization == "testOneRegi") {
- system(paste0("sed -i 's/__JOB_NAME__/REMIND_", cfg$title,"/g' submit_short.cmd"))
- system("sbatch submit_short.cmd")
- } else {
- system(paste0("sed -i 's/__JOB_NAME__/REMIND_", cfg$title,"/g' submit.cmd"))
- if (cfg$gms$cm_startyear > 2030) {
- system("sbatch --partition=ram_gpu submit.cmd")
- } else {
- system("sbatch submit.cmd")
- }
- }
- } else {
- # execute directly
- system("Rscript submit.R")
- }
-
- # on.exit sets working directory back to REMIND main folder
- return(cfg$results_folder)
-}
-
-getReportData <- function(rep,scen,inputpath_mag="magpie",inputpath_acc="costs") {
- require(lucode, quietly = TRUE,warn.conflicts =FALSE)
- require(magclass, quietly = TRUE,warn.conflicts =FALSE)
- .bioenergy_price <- function(mag){
- notGLO <- getRegions(mag)[!(getRegions(mag)=="GLO")]
- if("Demand|Bioenergy|++|2nd generation (EJ/yr)" %in% getNames(mag)) {
- # MAgPIE 4
- out <- mag[,,"Prices|Bioenergy (US$05/GJ)"]*0.0315576 # with transformation factor from US$2005/GJ to US$2005/Wa
- } else {
- # MAgPIE 3
- out <- mag[,,"Price|Primary Energy|Biomass (US$2005/GJ)"]*0.0315576 # with transformation factor from US$2005/GJ to US$2005/Wa
- }
- out["JPN",is.na(out["JPN",,]),] <- 0
- dimnames(out)[[3]] <- NULL #Delete variable name to prevent it from being written into output file
- write.magpie(out[notGLO,,],paste0("./modules/30_biomass/",inputpath_mag,"/input/p30_pebiolc_pricemag_coupling.csv"),file_type="csvr")
- }
- .bioenergy_costs <- function(mag){
- notGLO <- getRegions(mag)[!(getRegions(mag)=="GLO")]
- if ("Production Cost|Agriculture|Biomass|Energy Crops (million US$2005/yr)" %in% getNames(mag)) {
- out <- mag[,,"Production Cost|Agriculture|Biomass|Energy Crops (million US$2005/yr)"]/1000/1000 # with transformation factor from 10E6 US$2005 to 10E12 US$2005
- }
- else {
- # in old MAgPIE reports the unit is reported to be "billion", however the values are in million
- out <- mag[,,"Production Cost|Agriculture|Biomass|Energy Crops (billion US$2005/yr)"]/1000/1000 # with transformation factor from 10E6 US$2005 to 10E12 US$2005
- }
- out["JPN",is.na(out["JPN",,]),] <- 0
- dimnames(out)[[3]] <- NULL
- write.magpie(out[notGLO,,],paste0("./modules/30_biomass/",inputpath_mag,"/input/p30_pebiolc_costsmag.csv"),file_type="csvr")
- }
- .bioenergy_production <- function(mag){
- notGLO <- getRegions(mag)[!(getRegions(mag)=="GLO")]
- if("Demand|Bioenergy|2nd generation|++|Bioenergy crops (EJ/yr)" %in% getNames(mag)) {
- # MAgPIE 4
- out <- mag[,,"Demand|Bioenergy|2nd generation|++|Bioenergy crops (EJ/yr)"]/31.536 # EJ to TWa
- } else {
- # MAgPIE 3
- out <- mag[,,"Primary Energy Production|Biomass|Energy Crops (EJ/yr)"]/31.536 # EJ to TWa
- }
- out[which(out<0)] <- 0 # set negative values to zero since they cause errors in GMAS power function
- out["JPN",is.na(out["JPN",,]),] <- 0
- dimnames(out)[[3]] <- NULL
- write.magpie(out[notGLO,,],paste0("./modules/30_biomass/",inputpath_mag,"/input/p30_pebiolc_demandmag_coupling.csv"),file_type="csvr")
- }
- .emissions_mac <- function(mag) {
- # define three columns of dataframe:
- # emirem (remind emission names)
- # emimag (magpie emission names)
- # factor_mag2rem (factor for converting magpie to remind emissions)
- # 1/1000*28/44, # kt N2O/yr -> Mt N2O/yr -> Mt N/yr
- # 28/44, # Tg N2O/yr = Mt N2O/yr -> Mt N/yr
- # 1/1000*12/44, # Mt CO2/yr -> Gt CO2/yr -> Gt C/yr
- map <- data.frame(emirem=NULL,emimag=NULL,factor_mag2rem=NULL,stringsAsFactors=FALSE)
- if("Emissions|N2O|Land|Agriculture|+|Animal Waste Management (Mt N2O/yr)" %in% getNames(mag)) {
- # MAgPIE 4
- map <- rbind(map,data.frame(emimag="Emissions|CO2|Land (Mt CO2/yr)", emirem="co2luc", factor_mag2rem=1/1000*12/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land|Agriculture|+|Animal Waste Management (Mt N2O/yr)", emirem="n2oanwstm", factor_mag2rem=28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land|Agriculture|Agricultural Soils|+|Inorganic Fertilizers (Mt N2O/yr)", emirem="n2ofertin", factor_mag2rem=28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land|Agriculture|Agricultural Soils|+|Manure applied to Croplands (Mt N2O/yr)", emirem="n2oanwstc", factor_mag2rem=28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land|Agriculture|Agricultural Soils|+|Decay of Crop Residues (Mt N2O/yr)", emirem="n2ofertcr", factor_mag2rem=28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land|Agriculture|Agricultural Soils|+|Soil Organic Matter Loss (Mt N2O/yr)", emirem="n2ofertsom",factor_mag2rem=28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land|Agriculture|Agricultural Soils|+|Pasture (Mt N2O/yr)", emirem="n2oanwstp", factor_mag2rem=28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|CH4|Land|Agriculture|+|Rice (Mt CH4/yr)", emirem="ch4rice", factor_mag2rem=1,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|CH4|Land|Agriculture|+|Animal waste management (Mt CH4/yr)", emirem="ch4anmlwst",factor_mag2rem=1,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|CH4|Land|Agriculture|+|Enteric fermentation (Mt CH4/yr)", emirem="ch4animals",factor_mag2rem=1,stringsAsFactors=FALSE))
- } else {
- # MAgPIE 3
- map <- rbind(map,data.frame(emimag="Emissions|CO2|Land Use (Mt CO2/yr)", emirem="co2luc", factor_mag2rem=1/1000*12/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land Use|Agriculture|AWM (kt N2O/yr)", emirem="n2oanwstm", factor_mag2rem=1/1000*28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land Use|Agriculture|Cropland Soils|Inorganic Fertilizers (kt N2O/yr)", emirem="n2ofertin", factor_mag2rem=1/1000*28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land Use|Agriculture|Cropland Soils|Manure applied to Croplands (kt N2O/yr)", emirem="n2oanwstc", factor_mag2rem=1/1000*28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land Use|Agriculture|Cropland Soils|Decay of crop residues (kt N2O/yr)", emirem="n2ofertcr", factor_mag2rem=1/1000*28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land Use|Agriculture|Cropland Soils|Soil organic matter loss (kt N2O/yr)", emirem="n2ofertsom",factor_mag2rem=1/1000*28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land Use|Agriculture|Cropland Soils|Lower N2O emissions of rice (kt N2O/yr)", emirem="n2ofertrb", factor_mag2rem=1/1000*28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land Use|Agriculture|Pasture (kt N2O/yr)", emirem="n2oanwstp", factor_mag2rem=1/1000*28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land Use|Biomass Burning|Forest Burning (kt N2O/yr)", emirem="n2oforest", factor_mag2rem=1/1000*28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land Use|Biomass Burning|Savannah Burning (kt N2O/yr)", emirem="n2osavan", factor_mag2rem=1/1000*28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|N2O|Land Use|Biomass Burning|Agricultural Waste Burning (kt N2O/yr)", emirem="n2oagwaste",factor_mag2rem=1/1000*28/44,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|CH4|Land Use|Agriculture|Rice (Mt CH4/yr)", emirem="ch4rice", factor_mag2rem=1,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|CH4|Land Use|Agriculture|AWM (Mt CH4/yr)", emirem="ch4anmlwst",factor_mag2rem=1,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|CH4|Land Use|Agriculture|Enteric Fermentation (Mt CH4/yr)", emirem="ch4animals",factor_mag2rem=1,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|CH4|Land Use|Biomass Burning|Forest Burning (Mt CH4/yr)", emirem="ch4forest", factor_mag2rem=1,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|CH4|Land Use|Biomass Burning|Savannah Burning (Mt CH4/yr)", emirem="ch4savan", factor_mag2rem=1,stringsAsFactors=FALSE))
- map <- rbind(map,data.frame(emimag="Emissions|CH4|Land Use|Biomass Burning|Agricultural Waste Burning (Mt CH4/yr)", emirem="ch4agwaste",factor_mag2rem=1,stringsAsFactors=FALSE))
- }
-
- # Read data from MAgPIE report and convert to REMIND data, collect in 'out' object
- out<-NULL
- for (i in 1:nrow(map)) {
- tmp<-setNames(mag[,,map[i,]$emimag],map[i,]$emirem)
- tmp<-tmp*map[i,]$factor_mag2rem
- #tmp["JPN",is.na(tmp["JPN",,]),] <- 0
- # preliminary fix 20160111
- #cat("Preliminary quick fix: filtering out NAs for all and negative values for almost all landuse emissions except for co2luc and n2ofertrb\n")
- #tmp[is.na(tmp)] <- 0
- # preliminary 20160114: filter out negative values except for co2luc and n2ofertrb
- #if (map[i,]$emirem!="co2luc" && map[i,]$emirem!="n2ofertrb") {
- # tmp[tmp<0] <- 0
- #}
- out<-mbind(out,tmp)
- }
-
- # Write REMIND input file
- notGLO <- getRegions(mag)[!(getRegions(mag)=="GLO")]
- filename <- paste0("./core/input/f_macBaseMagpie_coupling.cs4r")
- write.magpie(out[notGLO],filename)
- write(paste0("*** EOF ",filename," ***"),file=filename,append=TRUE)
- }
- .agriculture_costs <- function(mag){
- notGLO <- getRegions(mag)[!(getRegions(mag)=="GLO")]
- out <- mag[,,"Costs|MainSolve w/o GHG Emissions (million US$05/yr)"]/1000/1000 # with transformation factor from 10E6 US$2005 to 10E12 US$2005
- out["JPN",is.na(out["JPN",,]),] <- 0
- dimnames(out)[[3]] <- NULL #Delete variable name to prevent it from being written into output file
- write.magpie(out[notGLO,,],paste0("./modules/26_agCosts/",inputpath_acc,"/input/p26_totLUcost_coupling.csv"),file_type="csvr")
- }
- .agriculture_tradebal <- function(mag){
- notGLO <- getRegions(mag)[!(getRegions(mag)=="GLO")]
- out <- mag[,,"Trade|Agriculture|Trade Balance (billion US$2005/yr)"]/1000 # with transformation factor from 10E9 US$2005 to 10E12 US$2005
- out["JPN",is.na(out["JPN",,]),] <- 0
- dimnames(out)[[3]] <- NULL
- write.magpie(out[notGLO,,],paste0("./modules/26_agCosts/",inputpath_acc,"/input/trade_bal_reg.rem.csv"),file_type="csvr")
- }
-
- if (length(scen)!=1) stop("getReportData: 'scen' does not contain exactly one scenario:",scen)
- if (length(intersect(scen,getNames(rep,dim="scenario")))!=1) stop("getReportData: 'scen'",scen," not contained in 'rep'.")
- rep <- collapseNames(rep) # get rid of scenrio and model dimension if they exist
- years <- 2000+5*(1:30)
- mag <- time_interpolate(rep,years)
- .bioenergy_price(mag)
- #.bioenergy_costs(mag) # Obsolete since bioenergy costs are not calculated by MAgPIE anymore but by integrating the supplycurve
- .bioenergy_production(mag)
- .emissions_mac(mag)
- .agriculture_costs(mag)
- # need to be updated to MAgPIE 4 interface
- #.agriculture_tradebal(mag)
-}
-
-start_reportrun <- function (cfg,path_report,sceninreport=NULL){
- rep <- convert.report(path_report,outmodel="REMIND")
- write.report(rep,"report.mif")
- if (!is.null(sceninreport))
- sceninreport <- intersect(sceninreport,names(rep))
- else
- sceninreport <- names(rep)
-
- for(scen in sceninreport) {
- cfg$title <- scen
- # If REMIND had pre-defined scenarios like MAgPIE they must be set here according to the scenario read in from the MAgPIE reporting
- # cfg <- setScenario(cfg,strsplit(scen,"_")[[1]][1])
- start_run(cfg, report=rep, sceninreport=scen)
- }
-}
diff --git a/start_bundle_climate.R b/start_bundle_climate.R
index fbbffd3..ab33cec 100644
--- a/start_bundle_climate.R
+++ b/start_bundle_climate.R
@@ -4,10 +4,15 @@
# | AGPL-3.0, you are granted additional permissions described in the
# | REMIND License Exception, version 1.0 (see LICENSE file).
# | Contact: remind@pik-potsdam.de
-source("scripts/start_functions.R")
require(lucode, quietly = TRUE, warn.conflicts = FALSE)
+source("scripts/start/submit.R")
+source("scripts/start/choose_slurmConfig.R")
+
+# Choose submission type
+slurmConfig <- choose_slurmConfig()
+
.setgdxcopy <- function(needle, stack, new) {
# delete entries in stack that contain needle and append new
out <- c(stack[-grep(needle, stack)], new)
@@ -55,6 +60,7 @@ for (scen in rownames(scenarios)) {
source("config/default.cfg")
# Have the log output written in a file (not on the screen)
+ cfg$slurmConfig <- slurmConfig
cfg$logoption <- 2
cfg$sequential <- NA
@@ -124,6 +130,6 @@ for (scen in rownames(scenarios)) {
| is.na(settings[scen,"path_gdx_ref"])){
cat("Starting: ",scen,"\n")
load(paste0(scen,".RData"))
- start_run(cfg)
+ submit(cfg)
}
}
--
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